A synthesis and subgroup analysis of the eosinophilic esophagitis tissue transcriptome

BACKGROUND

Eosinophilic esophagitis (EoE) is a chronic immune mediated inflammatory disorder of the esophagus. It is still unknown why children and adults present differently, and there is little evidence about why it is more common in men than women.

OBJECTIVE

Our aim was to synthesize published and unpublished esophageal bulk RNA-sequencing (RNA-seq) data to gain novel insights into the pathobiology of EoE and examine the differences in EoE transcriptome by sex and age group.

METHODS

Esophageal bulk RNA-seq data from 5 published and 2 unpublished studies resulting in 137 subjects (EoE: N = 76; controls: N = 61) were analyzed. For overall analysis, combined RNA-seq data of patients with EoE were compared with those of controls and subgroup analysis was conducted in patients with EoE by age of the patient (children [<18 years] vs adults [≥18 years]) and sex (female vs male). Gene-set enrichment analysis, ingenuity pathway analysis (IPA), cell-type analysis, immunohistochemistry, and T-cell or B-cell receptor analysis were performed.

RESULTS

Overall analysis identified dysregulation of new genes in EoE compared with controls. IPA revealed that EoE is characterized by a mixed inflammatory response compared with controls. Cell-type analysis showed that cell composition varied with age: children had more mast cells, whereas adults had more macrophages. Finally, gene-set enrichment analysis and IPA revealed pathways that were differentially regulated in adults versus children and male versus female patients with EoE.

CONCLUSIONS

Using a unique approach to analyze bulk RNA-seq data, we found that EoE is characterized by a mixed inflammatory response, and the EoE transcriptome may be influenced by age and sex. These findings enhance insights into the molecular mechanisms of EoE.

MTGR1 is required to maintain small intestinal stem cell populations

Undifferentiated intestinal stem cells (ISCs), particularly those marked by Lgr5, are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis, where they differentiate into a variety of specialized cell types. This process requires coordinated execution of complex transcriptional programs, which allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Thus, disrupting these programs may negatively impact homeostasis and response to injury. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss on ISC biology and differentiation programs. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic analyses revealed MTGR1 loss may instead promote stem cell differentiation into transit-amplifying cells at the expense of cycling ISC populations. Furthermore, ex vivo intestinal organoids established from Mtgr1 null were found nearly completely unable to survive and expand, likely due to aberrant ISC differentiation, suggesting that Mtgr1 null ISCs were functionally deficient as compared to WT ISCs. Together, these results identify a novel role for MTGR1 in ISC function and suggest that MTGR1 is required to maintain the undifferentiated state.

Abstract PO-051: Tumor stem cells arising from a non-stem origin maintain a differentiated phenotype and modulate T cell activity

Tumor stem cells (TSCs) contribute to cancer mortality via therapeutic resistance, tumor recurrence, and metastatic mechanisms. However, the origins of the stem capacity to TSCs remains in question, but all TSCs descend from the original tumor cell-of-origin where the first oncogenic event occurred. Tumors arising from different cells-of-origin are histologically identical, but it is unknown whether TSCs that arose from different origins are molecularly and functionally distinct. Using mouse models driving identical Apc mutations from Lrig1-expressing and Mist1-expressing cells, we characterized TSCs of tumors driven from stem and non-stem cells-of-origin using single cell RNA sequencing (scRNA-seq), organoids, and multiplexed imaging. We revealed reduced stem capacity but increased class II antigen presentation ability for non-stem cell (Mist1) driven TSCs compared with stem cell (Lrig1) driven TSCs, which resulted in a favorable immune microenvironment skewed towards active cytotoxic response in Mist1-driven tumors. These results suggest that the cell-of-origin of tumorigenesis provides a specific context by which TSCs are generated, dictating their interactions with the tumor microenvironment.

Citation Format: Cherie’ R. Scurrah, Bob Chen, Nick Markham, Alan Simmons, Austin Southard-Smith, Mary Macedonia, Eunyoung Choi, Qi Liu, Kay Washington, Bob Coffey, Jeremy Goettel, Ken Lau. Tumor stem cells arising from a non-stem origin maintain a differentiated phenotype and modulate T cell activity [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-051.

Colitis in mice with WASP deficiency in innate immune cells is associated with impairment in IL-10 production (71.10)

Colitis occurs in mice and some patients deficient in the Wiskott-Aldrich Syndrome protein (WASP), a hematopoietic-specific molecule that regulates the actin cytoskeleton. This colitis is lymphocyte-dependent, but severe disease is observed in chimeric mice with WT T cells and WASP KO innate immune cells, generated by transfer of WT CD4+ T cells into WASP/RAG DKO mice. Given the immunomodulatory function of IL-10, coupled with our findings that mixed bone marrow chimeras are free of colitis, we investigated whether alterations in IL-10 play a role in our colitis model. We found reduced IL-10 transcript levels in mesenteric lymph nodes of chimeric mice. To tease out the cellular source of decreased IL-10 production, WASP/RAG DKO DCs were stimulated in vitro and observed to produce less IL-10. We then transferred IL-10GFP CD4+ cells and found a reduction in the IL-10-expressing proportion of T cells in WASP/RAG DKO compared to RAG KO mice. Lastly, exogenous administration of IL-10-Ig completely abrogated disease in chimeric mice. In summary, besides impaired Treg homeostasis and function, severe colitis in our chimeric mice is associated with reduced IL-10 production in MLNs and in vitro stimulated DCs. Taken together with prevention of disease with IL-10 treatment, colitis in this model may result from decreased IL-10 production by WASP KO innate immune cells.